From 09b9008d785eeb194b82a44f2cbdd40e8e773139 Mon Sep 17 00:00:00 2001
From: Imad Bourouche <ji_bourouche@esi.dz>
Date: Fri, 6 Dec 2024 13:56:27 +0100
Subject: [PATCH 01/11] add capistrano deployment to ncbo cron to test locally

---
 Capfile                     |  41 ++++++++++++
 Gemfile                     |   4 ++
 config/deploy.rb            | 123 ++++++++++++++++++++++++++++++++++++
 config/deploy/production.rb |  61 ++++++++++++++++++
 config/deploy/staging.rb    |  61 ++++++++++++++++++
 5 files changed, 290 insertions(+)
 create mode 100644 Capfile
 create mode 100644 config/deploy.rb
 create mode 100644 config/deploy/production.rb
 create mode 100644 config/deploy/staging.rb

diff --git a/Capfile b/Capfile
new file mode 100644
index 00000000..86f6468f
--- /dev/null
+++ b/Capfile
@@ -0,0 +1,41 @@
+require 'bundler/setup'
+# Load DSL and set up stages
+require "capistrano/setup"
+
+# Include default deployment tasks
+require "capistrano/deploy"
+
+# Load the SCM plugin appropriate to your project:
+#
+# require "capistrano/scm/hg"
+# install_plugin Capistrano::SCM::Hg
+# or
+# require "capistrano/scm/svn"
+# install_plugin Capistrano::SCM::Svn
+# or
+require "capistrano/scm/git"
+install_plugin Capistrano::SCM::Git
+
+# Include tasks from other gems included in your Gemfile
+#
+# For documentation on these, see for example:
+#
+#   https://github.com/capistrano/rvm
+#   https://github.com/capistrano/rbenv
+#   https://github.com/capistrano/chruby
+#   https://github.com/capistrano/bundler
+#   https://github.com/capistrano/rails
+#   https://github.com/capistrano/passenger
+#
+# require "capistrano/rvm"
+require "capistrano/rbenv"
+# require "capistrano/chruby"
+require "capistrano/bundler"
+# require "capistrano/rails/assets"
+# require "capistrano/rails/migrations"
+# require "capistrano/passenger"
+require 'capistrano/locally'
+#require 'new_relic/recipes' # announce deployments in NewRelic
+
+# Load custom tasks from `lib/capistrano/tasks` if you have any defined
+Dir.glob("lib/capistrano/tasks/*.rake").each { |r| import r }
diff --git a/Gemfile b/Gemfile
index dcaf2c45..16013056 100644
--- a/Gemfile
+++ b/Gemfile
@@ -40,4 +40,8 @@ group :test do
   gem 'test-unit-minitest'
 end
 
+gem 'capistrano-bundler', require: false
+gem 'capistrano-locally', require: false
+gem 'capistrano-rbenv', require: false
+
 gem "binding_of_caller", "~> 1.0"
diff --git a/config/deploy.rb b/config/deploy.rb
new file mode 100644
index 00000000..3a93d0f9
--- /dev/null
+++ b/config/deploy.rb
@@ -0,0 +1,123 @@
+# config valid for current version and patch releases of Capistrano
+lock "~> 3.19.2"
+
+set :author, "imadbourouche"
+set :application, "ncbo_cron"
+set :repo_url, "https://github.com/#{fetch(:author)}/#{fetch(:application)}.git"
+
+set :deploy_via, :remote_cache
+
+# Default branch is :master
+# ask :branch, `git rev-parse --abbrev-ref HEAD`.chomp
+
+# Default deploy_to directory is /var/www/my_app_name
+set :deploy_to, "/home/bourouch/capistrano_deploy_test/#{fetch(:application)}"
+
+# Default value for :log_level is :debug
+set :log_level, :error
+
+# Default value for :linked_files is []
+# append :linked_files, "config/database.yml", 'config/master.key'
+
+# Default value for linked_dirs is []
+# set :linked_dirs, %w{log tmp/pids tmp/cache tmp/sockets vendor/bundle public/system}
+set :linked_dirs, %w{log vendor/bundle tmp/pids tmp/sockets public/system}
+
+
+# Default value for keep_releases is 5
+set :keep_releases, 5
+set :config_folder_path, "#{fetch(:application)}/#{fetch(:stage)}"
+
+
+# If you want to restart using `touch tmp/restart.txt`, add this to your config/deploy.rb:
+
+SSH_JUMPHOST = ENV.include?('SSH_JUMPHOST') ? ENV['SSH_JUMPHOST'] : 'jumpbox.hostname.com'
+SSH_JUMPHOST_USER = ENV.include?('SSH_JUMPHOST_USER') ? ENV['SSH_JUMPHOST_USER'] : 'username'
+
+# JUMPBOX_PROXY = "#{SSH_JUMPHOST_USER}@#{SSH_JUMPHOST}"
+# set :ssh_options, {
+#   user: 'ontoportal',
+#   forward_agent: 'true',
+#   # keys: %w(config/deploy_id_rsa),
+#   auth_methods: %w(publickey),
+#   # use ssh proxy if API servers are on a private network
+#   proxy: Net::SSH::Proxy::Command.new("ssh #{JUMPBOX_PROXY} -W %h:%p")
+# }
+
+# private git repo for configuraiton
+#PRIVATE_CONFIG_REPO = ENV.include?('PRIVATE_CONFIG_REPO') ? ENV['PRIVATE_CONFIG_REPO'] : 'https://your_github_pat_token@github.com/your_organization/ontoportal-configs.git'
+desc "Check if agent forwarding is working"
+task :forwarding do
+  on roles(:all) do |h|
+    if test("env | grep SSH_AUTH_SOCK")
+      info "Agent forwarding is up to #{h}"
+    else
+      error "Agent forwarding is NOT up to #{h}"
+    end
+  end
+end
+
+# inspired by http://nathaniel.talbott.ws/blog/2013/03/14/post-deploy-smoke-tests/
+desc 'Run smoke test'
+task :smoke_test do
+  on roles(:app) do
+    curl_opts = '--max-time 240 --connect-timeout 15 --retry 2'
+    failed_tests = []
+    curl_result = `ls #{fetch(:deploy_to)}`
+    failed_tests << 'smoke test FAILURE.' unless (curl_result != '')
+
+    if failed_tests.empty?
+      puts "smoke test passed on #{host}"
+    else
+      puts "\n\n****************************\n\n"
+      puts "SMOKE TEST FAILED on #{host}\n\n"
+      failed_tests.each do |failure|
+        puts failure
+      end
+      puts "\n\n****************************\n\n"
+    end
+  end
+end
+
+namespace :deploy do
+
+#   desc 'Incorporate the private repository content'
+#   # Get cofiguration from repo if PRIVATE_CONFIG_REPO env var is set
+#   # or get config from local directory if LOCAL_CONFIG_PATH env var is set
+#   task :get_config do
+#     if defined?(PRIVATE_CONFIG_REPO)
+#       TMP_CONFIG_PATH = "/tmp/#{SecureRandom.hex(15)}".freeze
+#       on roles(:app) do
+#         execute "git clone -q #{PRIVATE_CONFIG_REPO} #{TMP_CONFIG_PATH}"
+#         execute "rsync -av #{TMP_CONFIG_PATH}/#{fetch(:config_folder_path)}/ #{release_path}/"
+#         execute "rm -rf #{TMP_CONFIG_PATH}"
+#       end
+#     elsif defined?(LOCAL_CONFIG_PATH)
+#       on roles(:app) do
+#         execute "rsync -av #{LOCAL_CONFIG_PATH}/#{fetch(:application)}/ #{release_path}/"
+#       end
+#     end
+#   end
+
+  desc 'Restart application'
+  task :restart do
+    on roles(:app), in: :sequence, wait: 5 do
+      # Your restart mechanism here, for example:
+      # execute :touch, release_path.join('tmp/restart.txt')
+      execute 'ls /home/bourouch/capistrano_deploy_test'
+      execute 'sleep 5'
+    end
+  end
+
+  #after :updating, :get_config
+  after :publishing, :restart
+
+#   after :restart, :clear_cache do
+#     on roles(:web), in: :groups, limit: 3, wait: 10 do
+#       # Here we can do anything such as:
+#       # within release_path do
+#       #   execute :rake, 'cache:clear'
+#       # end
+#     end
+#   end
+end
diff --git a/config/deploy/production.rb b/config/deploy/production.rb
new file mode 100644
index 00000000..e892522a
--- /dev/null
+++ b/config/deploy/production.rb
@@ -0,0 +1,61 @@
+# server-based syntax
+# ======================
+# Defines a single server with a list of roles and multiple properties.
+# You can define all roles on a single server, or split them:
+
+# server "example.com", user: "deploy", roles: %w{app db web}, my_property: :my_value
+# server "example.com", user: "deploy", roles: %w{app web}, other_property: :other_value
+# server "db.example.com", user: "deploy", roles: %w{db}
+
+
+
+# role-based syntax
+# ==================
+
+# Defines a role with one or multiple servers. The primary server in each
+# group is considered to be the first unless any hosts have the primary
+# property set. Specify the username and a domain or IP for the server.
+# Don't use `:all`, it's a meta role.
+role :app, %w{127.0.0.1}
+#role :db, %w[agroportal.lirmm.fr] # sufficient to run db:migrate only on one system
+set :branch, ENV.include?('BRANCH') ? ENV['BRANCH'] : 'master'
+
+
+
+# Configuration
+# =============
+# You can set any configuration variable like in config/deploy.rb
+# These variables are then only loaded and set in this stage.
+# For available Capistrano configuration variables see the documentation page.
+# http://capistranorb.com/documentation/getting-started/configuration/
+# Feel free to add new variables to customise your setup.
+
+
+
+# Custom SSH Options
+# ==================
+# You may pass any option but keep in mind that net/ssh understands a
+# limited set of options, consult the Net::SSH documentation.
+# http://net-ssh.github.io/net-ssh/classes/Net/SSH.html#method-c-start
+#
+# Global options
+# --------------
+#  set :ssh_options, {
+#    keys: %w(/home/user_name/.ssh/id_rsa),
+#    forward_agent: false,
+#    auth_methods: %w(password)
+#  }
+#
+# The server-based syntax can be used to override options:
+# ------------------------------------
+# server "example.com",
+#   user: "user_name",
+#   roles: %w{web app},
+#   ssh_options: {
+#     user: "user_name", # overrides user setting above
+#     keys: %w(/home/user_name/.ssh/id_rsa),
+#     forward_agent: false,
+#     auth_methods: %w(publickey password)
+#     # password: "please use keys"
+#   }
+set :log_level, :error
\ No newline at end of file
diff --git a/config/deploy/staging.rb b/config/deploy/staging.rb
new file mode 100644
index 00000000..eed0ebdb
--- /dev/null
+++ b/config/deploy/staging.rb
@@ -0,0 +1,61 @@
+# server-based syntax
+# ======================
+# Defines a single server with a list of roles and multiple properties.
+# You can define all roles on a single server, or split them:
+
+# server "example.com", user: "deploy", roles: %w{app db web}, my_property: :my_value
+# server "example.com", user: "deploy", roles: %w{app web}, other_property: :other_value
+# server "db.example.com", user: "deploy", roles: %w{db}
+
+
+
+# role-based syntax
+# ==================
+
+# Defines a role with one or multiple servers. The primary server in each
+# group is considered to be the first unless any hosts have the primary
+# property set. Specify the username and a domain or IP for the server.
+# Don't use `:all`, it's a meta role.
+role :app, %w{127.0.0.1}
+#role :db, %w[agroportal.lirmm.fr] # sufficient to run db:migrate only on one system
+set :branch, ENV.include?('BRANCH') ? ENV['BRANCH'] : 'development'
+
+
+
+# Configuration
+# =============
+# You can set any configuration variable like in config/deploy.rb
+# These variables are then only loaded and set in this stage.
+# For available Capistrano configuration variables see the documentation page.
+# http://capistranorb.com/documentation/getting-started/configuration/
+# Feel free to add new variables to customise your setup.
+
+
+
+# Custom SSH Options
+# ==================
+# You may pass any option but keep in mind that net/ssh understands a
+# limited set of options, consult the Net::SSH documentation.
+# http://net-ssh.github.io/net-ssh/classes/Net/SSH.html#method-c-start
+#
+# Global options
+# --------------
+#  set :ssh_options, {
+#    keys: %w(/home/user_name/.ssh/id_rsa),
+#    forward_agent: false,
+#    auth_methods: %w(password)
+#  }
+#
+# The server-based syntax can be used to override options:
+# ------------------------------------
+# server "example.com",
+#   user: "user_name",
+#   roles: %w{web app},
+#   ssh_options: {
+#     user: "user_name", # overrides user setting above
+#     keys: %w(/home/user_name/.ssh/id_rsa),
+#     forward_agent: false,
+#     auth_methods: %w(publickey password)
+#     # password: "please use keys"
+#   }
+set :log_level, :error
\ No newline at end of file

From 60f711cc23539034736df8bba039d608d7714689 Mon Sep 17 00:00:00 2001
From: Imad Bourouche <ji_bourouche@esi.dz>
Date: Tue, 10 Dec 2024 10:25:37 +0100
Subject: [PATCH 02/11] add deployment group in Gemfile

---
 .gitignore       |  2 ++
 Capfile          |  1 -
 Gemfile          | 12 +++++++++---
 config/deploy.rb |  3 ---
 4 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/.gitignore b/.gitignore
index 3fdd0c6d..4c1af01d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -15,6 +15,8 @@ repo*
 .DS_Store
 tmp
 
+vendor/bundle/*
+
 # Code coverage reports
 coverage*
 
diff --git a/Capfile b/Capfile
index 86f6468f..ea67e952 100644
--- a/Capfile
+++ b/Capfile
@@ -1,4 +1,3 @@
-require 'bundler/setup'
 # Load DSL and set up stages
 require "capistrano/setup"
 
diff --git a/Gemfile b/Gemfile
index 16013056..4410dcf8 100644
--- a/Gemfile
+++ b/Gemfile
@@ -40,8 +40,14 @@ group :test do
   gem 'test-unit-minitest'
 end
 
-gem 'capistrano-bundler', require: false
-gem 'capistrano-locally', require: false
-gem 'capistrano-rbenv', require: false
+group :deployment do
+  # bcrypt_pbkdf and ed35519 is required for capistrano deployments when using ed25519 keys; see https://github.com/miloserdow/capistrano-deploy/issues/42
+  gem 'bcrypt_pbkdf', '>= 1.0', '< 2.0', require: false
+  gem 'capistrano', '~> 3', require: false
+  gem 'capistrano-bundler', require: false
+  gem 'capistrano-locally', require: false
+  gem 'capistrano-rbenv', require: false
+  gem 'ed25519', '>= 1.2', '< 2.0', require: false
+end
 
 gem "binding_of_caller", "~> 1.0"
diff --git a/config/deploy.rb b/config/deploy.rb
index 3a93d0f9..adb672ea 100644
--- a/config/deploy.rb
+++ b/config/deploy.rb
@@ -1,6 +1,3 @@
-# config valid for current version and patch releases of Capistrano
-lock "~> 3.19.2"
-
 set :author, "imadbourouche"
 set :application, "ncbo_cron"
 set :repo_url, "https://github.com/#{fetch(:author)}/#{fetch(:application)}.git"

From 26d64671e278062b0165ab213b3b08fadfd18e8e Mon Sep 17 00:00:00 2001
From: Imad Bourouche <ji_bourouche@esi.dz>
Date: Tue, 10 Dec 2024 10:25:47 +0100
Subject: [PATCH 03/11] update Gemfile.lock

---
 Gemfile.lock | 80 +++++++++++++++++++++++++++++++++++++---------------
 1 file changed, 58 insertions(+), 22 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 8007b8cd..143ba800 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -29,7 +29,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: c0f8697529ebfca2c3fe90d46d9482ac72f13362
+  revision: aff7843c7f2d8b2334a21e0f05599494ffde1427
   branch: development
   specs:
     ontologies_linked_data (0.0.1)
@@ -74,17 +74,35 @@ PATH
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (3.2.22.5)
-      i18n (~> 0.6, >= 0.6.4)
-      multi_json (~> 1.0)
+    activesupport (4.0.13)
+      i18n (~> 0.6, >= 0.6.9)
+      minitest (~> 4.2)
+      multi_json (~> 1.3)
+      thread_safe (~> 0.1)
+      tzinfo (~> 0.3.37)
     addressable (2.8.7)
       public_suffix (>= 2.0.2, < 7.0)
+    airbrussh (1.5.3)
+      sshkit (>= 1.6.1, != 1.7.0)
     base64 (0.2.0)
     bcrypt (3.1.20)
+    bcrypt_pbkdf (1.1.1)
     bigdecimal (3.1.8)
     binding_of_caller (1.0.1)
       debug_inspector (>= 1.2.0)
     builder (3.3.0)
+    capistrano (3.19.2)
+      airbrussh (>= 1.0.0)
+      i18n
+      rake (>= 10.0.0)
+      sshkit (>= 1.9.0)
+    capistrano-bundler (2.1.1)
+      capistrano (~> 3.1)
+    capistrano-locally (0.3.0)
+      capistrano (~> 3.0)
+    capistrano-rbenv (2.2.0)
+      capistrano (~> 3.1)
+      sshkit (~> 1.3)
     coderay (1.1.3)
     concurrent-ruby (1.3.4)
     connection_pool (2.4.1)
@@ -94,6 +112,7 @@ GEM
     declarative (0.0.20)
     docile (1.4.1)
     domain_name (0.6.20240107)
+    ed25519 (1.3.0)
     email_spec (2.1.1)
       htmlentities (~> 4.3.3)
       launchy (~> 2.1)
@@ -105,7 +124,7 @@ GEM
     faraday-net_http (3.0.2)
     faraday-retry (2.2.1)
       faraday (~> 2.0)
-    ffi (1.17.0)
+    ffi (1.16.3)
     gapic-common (0.21.1)
       faraday (>= 1.9, < 3.a)
       faraday-retry (>= 1.0, < 3.a)
@@ -114,10 +133,10 @@ GEM
       googleapis-common-protos-types (>= 1.11.0, < 2.a)
       googleauth (~> 1.9)
       grpc (~> 1.59)
-    google-analytics-data (0.6.1)
+    google-analytics-data (0.6.0)
       google-analytics-data-v1beta (>= 0.11, < 2.a)
       google-cloud-core (~> 1.6)
-    google-analytics-data-v1beta (0.13.1)
+    google-analytics-data-v1beta (0.14.0)
       gapic-common (>= 0.21.1, < 2.a)
       google-cloud-errors (~> 1.0)
     google-apis-analytics_v3 (0.16.0)
@@ -136,7 +155,7 @@ GEM
     google-cloud-env (2.1.1)
       faraday (>= 1.0, < 3.a)
     google-cloud-errors (1.4.0)
-    google-protobuf (3.25.5-x86_64-linux)
+    google-protobuf (3.25.3)
     googleapis-common-protos (1.6.0)
       google-protobuf (>= 3.18, < 5.a)
       googleapis-common-protos-types (~> 1.7)
@@ -150,17 +169,17 @@ GEM
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
-    grpc (1.65.2-x86_64-linux)
+    grpc (1.65.2)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
     htmlentities (4.3.4)
     http-accept (1.7.0)
-    http-cookie (1.0.7)
+    http-cookie (1.0.8)
       domain_name (~> 0.5)
     httpclient (2.8.3)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.7.4)
+    json (2.9.0)
     json-canonicalization (0.4.0)
     json-ld (3.2.5)
       htmlentities (~> 4.3)
@@ -175,7 +194,7 @@ GEM
       addressable (~> 2.8)
     libxml-ruby (5.0.3)
     link_header (0.0.8)
-    logger (1.6.1)
+    logger (1.6.2)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.6.6)
@@ -184,28 +203,33 @@ GEM
     mime-types (3.6.0)
       logger
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.1001)
+    mime-types-data (3.2024.1203)
     mini_mime (1.1.5)
     minitest (4.7.5)
     mlanett-redis-lock (0.2.7)
       redis
     multi_json (1.15.0)
-    mutex_m (0.2.0)
-    net-http-persistent (4.0.4)
+    mutex_m (0.3.0)
+    net-http-persistent (4.0.5)
       connection_pool (~> 2.2)
+    net-scp (4.0.0)
+      net-ssh (>= 2.6.5, < 8.0.0)
+    net-sftp (4.0.0)
+      net-ssh (>= 5.0.0, < 8.0.0)
+    net-ssh (7.3.0)
     netrc (0.11.0)
-    oj (3.16.6)
+    oj (3.16.7)
       bigdecimal (>= 3.0)
       ostruct (>= 0.2)
     omni_logger (0.1.4)
       logger
     os (1.1.4)
-    ostruct (0.6.0)
+    ostruct (0.6.1)
     parallel (1.26.3)
     parseconfig (1.1.2)
     pony (1.13.1)
       mail (>= 2.0)
-    pry (0.14.2)
+    pry (0.15.0)
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.1.1)
@@ -267,24 +291,36 @@ GEM
       simplecov (~> 0.19)
     simplecov-html (0.13.1)
     simplecov_json_formatter (0.1.4)
+    sshkit (1.23.2)
+      base64
+      net-scp (>= 1.1.2)
+      net-sftp (>= 2.1.2)
+      net-ssh (>= 2.8.0)
+      ostruct
     sys-proctable (1.3.0)
       ffi (~> 1.1)
     systemu (2.6.5)
     test-unit-minitest (0.9.1)
       minitest (~> 4.7)
+    thread_safe (0.3.6)
     trailblazer-option (0.1.2)
-    tzinfo (2.0.6)
-      concurrent-ruby (~> 1.0)
+    tzinfo (0.3.62)
     uber (0.1.0)
     uuid (2.3.9)
       macaddr (~> 1.0)
 
 PLATFORMS
-  x86_64-linux
+  ruby
 
 DEPENDENCIES
+  bcrypt_pbkdf (>= 1.0, < 2.0)
   binding_of_caller (~> 1.0)
+  capistrano (~> 3)
+  capistrano-bundler
+  capistrano-locally
+  capistrano-rbenv
   cube-ruby
+  ed25519 (>= 1.2, < 2.0)
   email_spec
   ffi (~> 1.16.3)
   goo!
@@ -314,4 +350,4 @@ DEPENDENCIES
   test-unit-minitest
 
 BUNDLED WITH
-   2.3.15
+   2.1.4

From cea7830377259b6e268baaf197ff141a19e0cdfc Mon Sep 17 00:00:00 2001
From: Imad Bourouche <ji_bourouche@esi.dz>
Date: Wed, 11 Dec 2024 09:54:55 +0100
Subject: [PATCH 04/11] changing configurations

---
 config/deploy.rb            | 96 ++++++++++++++++---------------------
 config/deploy/agroportal.rb | 19 ++++++++
 config/deploy/production.rb | 61 -----------------------
 config/deploy/staging.rb    | 72 ++++++----------------------
 config/deploy/test.rb       | 19 ++++++++
 5 files changed, 94 insertions(+), 173 deletions(-)
 create mode 100644 config/deploy/agroportal.rb
 delete mode 100644 config/deploy/production.rb
 create mode 100644 config/deploy/test.rb

diff --git a/config/deploy.rb b/config/deploy.rb
index adb672ea..9e2c0e92 100644
--- a/config/deploy.rb
+++ b/config/deploy.rb
@@ -8,17 +8,17 @@
 # ask :branch, `git rev-parse --abbrev-ref HEAD`.chomp
 
 # Default deploy_to directory is /var/www/my_app_name
-set :deploy_to, "/home/bourouch/capistrano_deploy_test/#{fetch(:application)}"
+set :deploy_to, "/srv/ontoportal/#{fetch(:application)}"
 
 # Default value for :log_level is :debug
-set :log_level, :error
+set :log_level, :debug
 
 # Default value for :linked_files is []
 # append :linked_files, "config/database.yml", 'config/master.key'
 
 # Default value for linked_dirs is []
 # set :linked_dirs, %w{log tmp/pids tmp/cache tmp/sockets vendor/bundle public/system}
-set :linked_dirs, %w{log vendor/bundle tmp/pids tmp/sockets public/system}
+set :linked_dirs, %w{log logs vendor/bundle tmp/pids tmp/sockets public/system}
 
 
 # Default value for keep_releases is 5
@@ -31,15 +31,15 @@
 SSH_JUMPHOST = ENV.include?('SSH_JUMPHOST') ? ENV['SSH_JUMPHOST'] : 'jumpbox.hostname.com'
 SSH_JUMPHOST_USER = ENV.include?('SSH_JUMPHOST_USER') ? ENV['SSH_JUMPHOST_USER'] : 'username'
 
-# JUMPBOX_PROXY = "#{SSH_JUMPHOST_USER}@#{SSH_JUMPHOST}"
-# set :ssh_options, {
-#   user: 'ontoportal',
-#   forward_agent: 'true',
-#   # keys: %w(config/deploy_id_rsa),
-#   auth_methods: %w(publickey),
-#   # use ssh proxy if API servers are on a private network
-#   proxy: Net::SSH::Proxy::Command.new("ssh #{JUMPBOX_PROXY} -W %h:%p")
-# }
+JUMPBOX_PROXY = "#{SSH_JUMPHOST_USER}@#{SSH_JUMPHOST}"
+set :ssh_options, {
+  user: 'bourouch',
+  forward_agent: 'true',
+  keys: %w(config/deploy_id_rsa),
+  auth_methods: %w(publickey),
+  # use ssh proxy if API servers are on a private network
+  #proxy: Net::SSH::Proxy::Command.new("ssh #{JUMPBOX_PROXY} -W %h:%p")
+}
 
 # private git repo for configuraiton
 #PRIVATE_CONFIG_REPO = ENV.include?('PRIVATE_CONFIG_REPO') ? ENV['PRIVATE_CONFIG_REPO'] : 'https://your_github_pat_token@github.com/your_organization/ontoportal-configs.git'
@@ -54,67 +54,53 @@
   end
 end
 
-# inspired by http://nathaniel.talbott.ws/blog/2013/03/14/post-deploy-smoke-tests/
-desc 'Run smoke test'
+# Smoke test for checking if the service is up
+desc 'Smoke test: Check if ncbo_cron service is running'
 task :smoke_test do
-  on roles(:app) do
-    curl_opts = '--max-time 240 --connect-timeout 15 --retry 2'
-    failed_tests = []
-    curl_result = `ls #{fetch(:deploy_to)}`
-    failed_tests << 'smoke test FAILURE.' unless (curl_result != '')
-
-    if failed_tests.empty?
-      puts "smoke test passed on #{host}"
+  on roles(:app), in: :sequence, wait: 5 do
+    # Check if the service is running using systemctl
+    result = `systemctl is-active ncbo_cron`
+    if result.strip == 'active'
+      info "ncbo_cron service is up and running!"
     else
-      puts "\n\n****************************\n\n"
-      puts "SMOKE TEST FAILED on #{host}\n\n"
-      failed_tests.each do |failure|
-        puts failure
-      end
-      puts "\n\n****************************\n\n"
+      error "ncbo_cron service failed to start."
     end
   end
 end
 
 namespace :deploy do
 
-#   desc 'Incorporate the private repository content'
-#   # Get cofiguration from repo if PRIVATE_CONFIG_REPO env var is set
-#   # or get config from local directory if LOCAL_CONFIG_PATH env var is set
-#   task :get_config do
-#     if defined?(PRIVATE_CONFIG_REPO)
-#       TMP_CONFIG_PATH = "/tmp/#{SecureRandom.hex(15)}".freeze
-#       on roles(:app) do
-#         execute "git clone -q #{PRIVATE_CONFIG_REPO} #{TMP_CONFIG_PATH}"
-#         execute "rsync -av #{TMP_CONFIG_PATH}/#{fetch(:config_folder_path)}/ #{release_path}/"
-#         execute "rm -rf #{TMP_CONFIG_PATH}"
-#       end
-#     elsif defined?(LOCAL_CONFIG_PATH)
-#       on roles(:app) do
-#         execute "rsync -av #{LOCAL_CONFIG_PATH}/#{fetch(:application)}/ #{release_path}/"
-#       end
-#     end
-#   end
+  desc 'Incorporate the private repository content'
+  # Get cofiguration from repo if PRIVATE_CONFIG_REPO env var is set
+  # or get config from local directory if LOCAL_CONFIG_PATH env var is set
+  task :get_config do
+    if defined?(PRIVATE_CONFIG_REPO)
+      TMP_CONFIG_PATH = "/tmp/#{SecureRandom.hex(15)}".freeze
+      on roles(:app) do
+        execute "git clone -q #{PRIVATE_CONFIG_REPO} #{TMP_CONFIG_PATH}"
+        execute "rsync -av #{TMP_CONFIG_PATH}/#{fetch(:config_folder_path)}/ #{release_path}/"
+        execute "rm -rf #{TMP_CONFIG_PATH}"
+      end
+    elsif defined?(LOCAL_CONFIG_PATH)
+      on roles(:app) do
+        execute "rsync -av #{LOCAL_CONFIG_PATH}/#{fetch(:application)}/ #{release_path}/"
+      end
+    end
+  end
 
   desc 'Restart application'
   task :restart do
     on roles(:app), in: :sequence, wait: 5 do
       # Your restart mechanism here, for example:
       # execute :touch, release_path.join('tmp/restart.txt')
-      execute 'ls /home/bourouch/capistrano_deploy_test'
+      #execute 'sudo systemctl restart ncbo_cron'
+      execute 'ls /srv/ontoportal/ncbo_cron'
       execute 'sleep 5'
     end
   end
 
-  #after :updating, :get_config
+  after :updating, :get_config
   after :publishing, :restart
+  after :restart, :smoke_test
 
-#   after :restart, :clear_cache do
-#     on roles(:web), in: :groups, limit: 3, wait: 10 do
-#       # Here we can do anything such as:
-#       # within release_path do
-#       #   execute :rake, 'cache:clear'
-#       # end
-#     end
-#   end
 end
diff --git a/config/deploy/agroportal.rb b/config/deploy/agroportal.rb
new file mode 100644
index 00000000..47d337e9
--- /dev/null
+++ b/config/deploy/agroportal.rb
@@ -0,0 +1,19 @@
+# Simple Role Syntax
+# ==================
+# Supports bulk-adding hosts to roles, the primary
+# server in each group is considered to be the first
+# unless any hosts have the primary property set.
+# Don't declare `role :all`, it's a meta role
+#role :app, %w[agroportal.lirmm.fr]
+#role :db, %w[agroportal.lirmm.fr] # sufficient to run db:migrate only on one system
+role :app, %w{127.0.0.1}
+role :db, %w{127.0.0.1}
+set :branch, ENV.include?('BRANCH') ? ENV['BRANCH'] : 'master'
+# Extended Server Syntax
+# ======================
+# This can be used to drop a more detailed server
+# definition into the server list. The second argument
+# something that quacks like a hash can be used to set
+# extended properties on the server.
+# server 'example.com', user: 'deploy', roles: %w{web app}, my_property: :my_value
+set :log_level, :error
diff --git a/config/deploy/production.rb b/config/deploy/production.rb
deleted file mode 100644
index e892522a..00000000
--- a/config/deploy/production.rb
+++ /dev/null
@@ -1,61 +0,0 @@
-# server-based syntax
-# ======================
-# Defines a single server with a list of roles and multiple properties.
-# You can define all roles on a single server, or split them:
-
-# server "example.com", user: "deploy", roles: %w{app db web}, my_property: :my_value
-# server "example.com", user: "deploy", roles: %w{app web}, other_property: :other_value
-# server "db.example.com", user: "deploy", roles: %w{db}
-
-
-
-# role-based syntax
-# ==================
-
-# Defines a role with one or multiple servers. The primary server in each
-# group is considered to be the first unless any hosts have the primary
-# property set. Specify the username and a domain or IP for the server.
-# Don't use `:all`, it's a meta role.
-role :app, %w{127.0.0.1}
-#role :db, %w[agroportal.lirmm.fr] # sufficient to run db:migrate only on one system
-set :branch, ENV.include?('BRANCH') ? ENV['BRANCH'] : 'master'
-
-
-
-# Configuration
-# =============
-# You can set any configuration variable like in config/deploy.rb
-# These variables are then only loaded and set in this stage.
-# For available Capistrano configuration variables see the documentation page.
-# http://capistranorb.com/documentation/getting-started/configuration/
-# Feel free to add new variables to customise your setup.
-
-
-
-# Custom SSH Options
-# ==================
-# You may pass any option but keep in mind that net/ssh understands a
-# limited set of options, consult the Net::SSH documentation.
-# http://net-ssh.github.io/net-ssh/classes/Net/SSH.html#method-c-start
-#
-# Global options
-# --------------
-#  set :ssh_options, {
-#    keys: %w(/home/user_name/.ssh/id_rsa),
-#    forward_agent: false,
-#    auth_methods: %w(password)
-#  }
-#
-# The server-based syntax can be used to override options:
-# ------------------------------------
-# server "example.com",
-#   user: "user_name",
-#   roles: %w{web app},
-#   ssh_options: {
-#     user: "user_name", # overrides user setting above
-#     keys: %w(/home/user_name/.ssh/id_rsa),
-#     forward_agent: false,
-#     auth_methods: %w(publickey password)
-#     # password: "please use keys"
-#   }
-set :log_level, :error
\ No newline at end of file
diff --git a/config/deploy/staging.rb b/config/deploy/staging.rb
index eed0ebdb..5feb8c7c 100644
--- a/config/deploy/staging.rb
+++ b/config/deploy/staging.rb
@@ -1,61 +1,19 @@
-# server-based syntax
-# ======================
-# Defines a single server with a list of roles and multiple properties.
-# You can define all roles on a single server, or split them:
-
-# server "example.com", user: "deploy", roles: %w{app db web}, my_property: :my_value
-# server "example.com", user: "deploy", roles: %w{app web}, other_property: :other_value
-# server "db.example.com", user: "deploy", roles: %w{db}
-
-
-
-# role-based syntax
+# Simple Role Syntax
 # ==================
-
-# Defines a role with one or multiple servers. The primary server in each
-# group is considered to be the first unless any hosts have the primary
-# property set. Specify the username and a domain or IP for the server.
-# Don't use `:all`, it's a meta role.
+# Supports bulk-adding hosts to roles, the primary
+# server in each group is considered to be the first
+# unless any hosts have the primary property set.
+# Don't declare `role :all`, it's a meta role
+# role :app, %w{stageportal.lirmm.fr}
+# role :db, %w{stageportal.lirmm.fr} # sufficient to run db:migrate only on one system
 role :app, %w{127.0.0.1}
-#role :db, %w[agroportal.lirmm.fr] # sufficient to run db:migrate only on one system
+role :db, %w{127.0.0.1}
 set :branch, ENV.include?('BRANCH') ? ENV['BRANCH'] : 'development'
-
-
-
-# Configuration
-# =============
-# You can set any configuration variable like in config/deploy.rb
-# These variables are then only loaded and set in this stage.
-# For available Capistrano configuration variables see the documentation page.
-# http://capistranorb.com/documentation/getting-started/configuration/
-# Feel free to add new variables to customise your setup.
-
-
-
-# Custom SSH Options
-# ==================
-# You may pass any option but keep in mind that net/ssh understands a
-# limited set of options, consult the Net::SSH documentation.
-# http://net-ssh.github.io/net-ssh/classes/Net/SSH.html#method-c-start
-#
-# Global options
-# --------------
-#  set :ssh_options, {
-#    keys: %w(/home/user_name/.ssh/id_rsa),
-#    forward_agent: false,
-#    auth_methods: %w(password)
-#  }
-#
-# The server-based syntax can be used to override options:
-# ------------------------------------
-# server "example.com",
-#   user: "user_name",
-#   roles: %w{web app},
-#   ssh_options: {
-#     user: "user_name", # overrides user setting above
-#     keys: %w(/home/user_name/.ssh/id_rsa),
-#     forward_agent: false,
-#     auth_methods: %w(publickey password)
-#     # password: "please use keys"
-#   }
+# Extended Server Syntax
+# ======================
+# This can be used to drop a more detailed server
+# definition into the server list. The second argument
+# something that quacks like a hash can be used to set
+# extended properties on the server.
+#server 'example.com', user: 'deploy', roles: %w{web app}, my_property: :my_value
 set :log_level, :error
\ No newline at end of file
diff --git a/config/deploy/test.rb b/config/deploy/test.rb
new file mode 100644
index 00000000..650fa7cd
--- /dev/null
+++ b/config/deploy/test.rb
@@ -0,0 +1,19 @@
+# Simple Role Syntax
+# ==================
+# Supports bulk-adding hosts to roles, the primary
+# server in each group is considered to be the first
+# unless any hosts have the primary property set.
+# Don't declare `role :all`, it's a meta role
+# role :app, %w{testportal.lirmm.fr}
+# role :db, %w{testportal.lirmm.fr} # sufficient to run db:migrate only on one system
+role :app, %w{127.0.0.1}
+role :db, %w{127.0.0.1}
+set :branch, ENV.include?('BRANCH') ? ENV['BRANCH'] : 'feature/add-capistrano-deployment'
+# Extended Server Syntax
+# ======================
+# This can be used to drop a more detailed server
+# definition into the server list. The second argument
+# something that quacks like a hash can be used to set
+# extended properties on the server.
+#server 'example.com', user: 'deploy', roles: %w{web app}, my_property: :my_value
+set :log_level, :error
\ No newline at end of file

From d9f8135a9adf6142e118c802b13a60d5d4fa8d06 Mon Sep 17 00:00:00 2001
From: Imad Bourouche <ji_bourouche@esi.dz>
Date: Wed, 11 Dec 2024 09:55:06 +0100
Subject: [PATCH 05/11] update Gemfile.lock

---
 Gemfile.lock | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 143ba800..da234d90 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -29,7 +29,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: aff7843c7f2d8b2334a21e0f05599494ffde1427
+  revision: 6fd6960a1f134ec8c8aff07a5897bb0da12bcc8d
   branch: development
   specs:
     ontologies_linked_data (0.0.1)
@@ -254,7 +254,7 @@ GEM
       rexml (~> 3.2)
     redis (5.3.0)
       redis-client (>= 0.22.0)
-    redis-client (0.22.2)
+    redis-client (0.23.0)
       connection_pool
     representable (3.2.0)
       declarative (< 0.1.0)

From e45cf9b4d3e6e32ebb11ff7760e038f8f024acf6 Mon Sep 17 00:00:00 2001
From: Imad Bourouche <ji_bourouche@esi.dz>
Date: Wed, 11 Dec 2024 11:43:42 +0100
Subject: [PATCH 06/11] add deploy workflow

---
 .github/workflows/deploy.yml | 93 ++++++++++++++++++++++++++++++++++++
 1 file changed, 93 insertions(+)
 create mode 100644 .github/workflows/deploy.yml

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
new file mode 100644
index 00000000..a35bf88e
--- /dev/null
+++ b/.github/workflows/deploy.yml
@@ -0,0 +1,93 @@
+# Workflow to deploy NCBO Cron to stage/prod systems
+#
+# Required github secrets:
+#
+# CONFIG_REPO - github repo containing config and customizations for NCBO_CRON. Format 'author/private_config_repo'
+# it is used for getting capistrano deployment configuration for stages on the github actions runner and
+# PRIVATE_CONFIG_REPO env var is constructed from it which is used by capistrano on the API hosts for pulling configs.
+#
+# GH_PAT - github Personal Access Token for accessing private config repo
+#
+# SSH_JUMPHOST - ssh jump/proxy host though which deployments have to though if API nodes live on private network.
+# SSH_JUMPHOST_USER - username  to use to connect to the ssh jump/proxy.
+#
+# DEPLOY_ENC_KEY - key for decrypting deploymnet ssh key residing in config/
+# this SSH key is used for accessing jump host, API nodes, and private github repo.
+
+name: Capistrano Deployment
+# Controls when the action will run.
+on:
+  push:
+    branches:
+      - stage
+      - test
+  # Allows running this workflow manually from the Actions tab
+  workflow_dispatch:
+    inputs:
+      BRANCH:
+        description: "Branch/tag to deploy"
+        type: choice
+        options:
+          - stage
+          - test
+          - master
+        default: stage
+        required: true
+      environment:
+        description: "target environment to deploy to"
+        type: choice
+        options:
+          - staging
+          - test
+          - agroportal
+        default: stage
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    env:
+      BUNDLE_WITHOUT: default #install gems required primarely for deployment in order to speed up workflow
+      PRIVATE_CONFIG_REPO: ${{ format('git@github.com:{0}.git', secrets.CONFIG_REPO) }}
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      - name: set branch/tag and environment to deploy from inputs
+        run: |
+          # workflow_dispatch default input doesn't get set on push so we need to set defaults
+          # via shell parameter expansion       
+        
+          USER_INPUT_BRANCH="${{ inputs.branch || github.head_ref || 'master' }}"
+          echo "BRANCH=${USER_INPUT_BRANCH}" >> $GITHUB_ENV
+          
+          USER_INPUT_ENVIRONMENT=${{ inputs.environment }}
+          echo "TARGET=${USER_INPUT_ENVIRONMENT:-test}" >> $GITHUB_ENV
+
+          CONFIG_REPO=${{ secrets.CONFIG_REPO }}
+          GH_PAT=${{ secrets.GH_PAT }}
+          echo "PRIVATE_CONFIG_REPO=https://${GH_PAT}@github.com/${CONFIG_REPO}" >> $GITHUB_ENV
+
+          echo "SSH_JUMPHOST=${{ secrets.SSH_JUMPHOST }}" >> $GITHUB_ENV
+          echo "SSH_JUMPHOST_USER=${{ secrets.SSH_JUMPHOST_USER }}" >> $GITHUB_ENV
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v3
+      - uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: 2.7.8 # Not needed with a .ruby-version file
+          bundler-cache: true # runs 'bundle install' and caches installed gems automatically
+      - name: get-deployment-config
+        uses: actions/checkout@v3
+        with:
+          repository: ${{ secrets.CONFIG_REPO }} # repository containing deployment settings
+          token: ${{ secrets.GH_PAT }} # `GH_PAT` is a secret that contains your PAT
+          path: deploy_config
+      - name: copy-deployment-config
+        run: cp -r deploy_config/ncbo_cron/${{ inputs.environment }}/* .
+        # add ssh hostkey so that capistrano doesn't complain
+      - name: Add jumphost's hostkey to Known Hosts
+        run: |
+          mkdir -p ~/.ssh
+          echo "${{ secrets.SSH_JUMPHOST }}"
+          ssh-keyscan -H ${{ secrets.SSH_JUMPHOST }} > ~/.ssh/known_hosts
+        shell: bash
+      - uses: miloserdow/capistrano-deploy@master
+        with:
+          target: ${{ env.TARGET }} # which environment to deploy
+          deploy_key: ${{ secrets.DEPLOY_ENC_KEY }} # Name of the variable configured in Settings/Secrets of your github project
\ No newline at end of file

From b14dd2c27017bbb9a950beb6cadaeef0b67a1180 Mon Sep 17 00:00:00 2001
From: Imad Bourouche <ji_bourouche@esi.dz>
Date: Wed, 11 Dec 2024 16:24:52 +0100
Subject: [PATCH 07/11] Update Gemfile.lock

---
 Gemfile.lock | 43 ++++++++++++++++++++-----------------------
 1 file changed, 20 insertions(+), 23 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index da234d90..c0989308 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -29,7 +29,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: 6fd6960a1f134ec8c8aff07a5897bb0da12bcc8d
+  revision: c0f8697529ebfca2c3fe90d46d9482ac72f13362
   branch: development
   specs:
     ontologies_linked_data (0.0.1)
@@ -74,12 +74,9 @@ PATH
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (4.0.13)
-      i18n (~> 0.6, >= 0.6.9)
-      minitest (~> 4.2)
-      multi_json (~> 1.3)
-      thread_safe (~> 0.1)
-      tzinfo (~> 0.3.37)
+    activesupport (3.2.22.5)
+      i18n (~> 0.6, >= 0.6.4)
+      multi_json (~> 1.0)
     addressable (2.8.7)
       public_suffix (>= 2.0.2, < 7.0)
     airbrussh (1.5.3)
@@ -155,7 +152,7 @@ GEM
     google-cloud-env (2.1.1)
       faraday (>= 1.0, < 3.a)
     google-cloud-errors (1.4.0)
-    google-protobuf (3.25.3)
+    google-protobuf (3.25.3-x86_64-linux)
     googleapis-common-protos (1.6.0)
       google-protobuf (>= 3.18, < 5.a)
       googleapis-common-protos-types (~> 1.7)
@@ -169,17 +166,17 @@ GEM
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
-    grpc (1.65.2)
+    grpc (1.65.2-x86_64-linux)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
     htmlentities (4.3.4)
     http-accept (1.7.0)
-    http-cookie (1.0.8)
+    http-cookie (1.0.7)
       domain_name (~> 0.5)
     httpclient (2.8.3)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.9.0)
+    json (2.7.4)
     json-canonicalization (0.4.0)
     json-ld (3.2.5)
       htmlentities (~> 4.3)
@@ -194,7 +191,7 @@ GEM
       addressable (~> 2.8)
     libxml-ruby (5.0.3)
     link_header (0.0.8)
-    logger (1.6.2)
+    logger (1.6.1)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.6.6)
@@ -203,14 +200,14 @@ GEM
     mime-types (3.6.0)
       logger
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.1203)
+    mime-types-data (3.2024.1001)
     mini_mime (1.1.5)
     minitest (4.7.5)
     mlanett-redis-lock (0.2.7)
       redis
     multi_json (1.15.0)
-    mutex_m (0.3.0)
-    net-http-persistent (4.0.5)
+    mutex_m (0.2.0)
+    net-http-persistent (4.0.4)
       connection_pool (~> 2.2)
     net-scp (4.0.0)
       net-ssh (>= 2.6.5, < 8.0.0)
@@ -218,18 +215,18 @@ GEM
       net-ssh (>= 5.0.0, < 8.0.0)
     net-ssh (7.3.0)
     netrc (0.11.0)
-    oj (3.16.7)
+    oj (3.16.6)
       bigdecimal (>= 3.0)
       ostruct (>= 0.2)
     omni_logger (0.1.4)
       logger
     os (1.1.4)
-    ostruct (0.6.1)
+    ostruct (0.6.0)
     parallel (1.26.3)
     parseconfig (1.1.2)
     pony (1.13.1)
       mail (>= 2.0)
-    pry (0.15.0)
+    pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.1.1)
@@ -254,7 +251,7 @@ GEM
       rexml (~> 3.2)
     redis (5.3.0)
       redis-client (>= 0.22.0)
-    redis-client (0.23.0)
+    redis-client (0.22.2)
       connection_pool
     representable (3.2.0)
       declarative (< 0.1.0)
@@ -302,15 +299,15 @@ GEM
     systemu (2.6.5)
     test-unit-minitest (0.9.1)
       minitest (~> 4.7)
-    thread_safe (0.3.6)
     trailblazer-option (0.1.2)
-    tzinfo (0.3.62)
+    tzinfo (2.0.6)
+      concurrent-ruby (~> 1.0)
     uber (0.1.0)
     uuid (2.3.9)
       macaddr (~> 1.0)
 
 PLATFORMS
-  ruby
+  x86_64-linux
 
 DEPENDENCIES
   bcrypt_pbkdf (>= 1.0, < 2.0)
@@ -350,4 +347,4 @@ DEPENDENCIES
   test-unit-minitest
 
 BUNDLED WITH
-   2.1.4
+   2.3.15

From c18e510a740fc04de0928d68aa3e9e864f929faf Mon Sep 17 00:00:00 2001
From: Imad Bourouche <ji_bourouche@esi.dz>
Date: Fri, 13 Dec 2024 11:13:39 +0100
Subject: [PATCH 08/11] change configurations

---
 config/deploy.rb            | 11 +++++------
 config/deploy/agroportal.rb |  5 +----
 config/deploy/staging.rb    |  7 ++-----
 config/deploy/test.rb       |  7 ++-----
 4 files changed, 10 insertions(+), 20 deletions(-)

diff --git a/config/deploy.rb b/config/deploy.rb
index 9e2c0e92..b7d255a2 100644
--- a/config/deploy.rb
+++ b/config/deploy.rb
@@ -1,4 +1,4 @@
-set :author, "imadbourouche"
+set :author, "ontoportal-lirmm"
 set :application, "ncbo_cron"
 set :repo_url, "https://github.com/#{fetch(:author)}/#{fetch(:application)}.git"
 
@@ -18,7 +18,7 @@
 
 # Default value for linked_dirs is []
 # set :linked_dirs, %w{log tmp/pids tmp/cache tmp/sockets vendor/bundle public/system}
-set :linked_dirs, %w{log logs vendor/bundle tmp/pids tmp/sockets public/system}
+set :linked_dirs, %w{log vendor/bundle tmp/pids tmp/sockets public/system}
 
 
 # Default value for keep_releases is 5
@@ -33,12 +33,12 @@
 
 JUMPBOX_PROXY = "#{SSH_JUMPHOST_USER}@#{SSH_JUMPHOST}"
 set :ssh_options, {
-  user: 'bourouch',
+  user: 'ontoportal',
   forward_agent: 'true',
   keys: %w(config/deploy_id_rsa),
   auth_methods: %w(publickey),
   # use ssh proxy if API servers are on a private network
-  #proxy: Net::SSH::Proxy::Command.new("ssh #{JUMPBOX_PROXY} -W %h:%p")
+  proxy: Net::SSH::Proxy::Command.new("ssh #{JUMPBOX_PROXY} -W %h:%p")
 }
 
 # private git repo for configuraiton
@@ -93,8 +93,7 @@
     on roles(:app), in: :sequence, wait: 5 do
       # Your restart mechanism here, for example:
       # execute :touch, release_path.join('tmp/restart.txt')
-      #execute 'sudo systemctl restart ncbo_cron'
-      execute 'ls /srv/ontoportal/ncbo_cron'
+      execute 'sudo systemctl restart ncbo_cron'
       execute 'sleep 5'
     end
   end
diff --git a/config/deploy/agroportal.rb b/config/deploy/agroportal.rb
index 47d337e9..0ce7bb55 100644
--- a/config/deploy/agroportal.rb
+++ b/config/deploy/agroportal.rb
@@ -4,10 +4,7 @@
 # server in each group is considered to be the first
 # unless any hosts have the primary property set.
 # Don't declare `role :all`, it's a meta role
-#role :app, %w[agroportal.lirmm.fr]
-#role :db, %w[agroportal.lirmm.fr] # sufficient to run db:migrate only on one system
-role :app, %w{127.0.0.1}
-role :db, %w{127.0.0.1}
+role :app, %w[agroportal.lirmm.fr]
 set :branch, ENV.include?('BRANCH') ? ENV['BRANCH'] : 'master'
 # Extended Server Syntax
 # ======================
diff --git a/config/deploy/staging.rb b/config/deploy/staging.rb
index 5feb8c7c..8e2db320 100644
--- a/config/deploy/staging.rb
+++ b/config/deploy/staging.rb
@@ -4,11 +4,8 @@
 # server in each group is considered to be the first
 # unless any hosts have the primary property set.
 # Don't declare `role :all`, it's a meta role
-# role :app, %w{stageportal.lirmm.fr}
-# role :db, %w{stageportal.lirmm.fr} # sufficient to run db:migrate only on one system
-role :app, %w{127.0.0.1}
-role :db, %w{127.0.0.1}
-set :branch, ENV.include?('BRANCH') ? ENV['BRANCH'] : 'development'
+role :app, %w{stageportal.lirmm.fr}
+set :branch, ENV.include?('BRANCH') ? ENV['BRANCH'] : 'stage'
 # Extended Server Syntax
 # ======================
 # This can be used to drop a more detailed server
diff --git a/config/deploy/test.rb b/config/deploy/test.rb
index 650fa7cd..8fc790cb 100644
--- a/config/deploy/test.rb
+++ b/config/deploy/test.rb
@@ -4,11 +4,8 @@
 # server in each group is considered to be the first
 # unless any hosts have the primary property set.
 # Don't declare `role :all`, it's a meta role
-# role :app, %w{testportal.lirmm.fr}
-# role :db, %w{testportal.lirmm.fr} # sufficient to run db:migrate only on one system
-role :app, %w{127.0.0.1}
-role :db, %w{127.0.0.1}
-set :branch, ENV.include?('BRANCH') ? ENV['BRANCH'] : 'feature/add-capistrano-deployment'
+role :app, %w{testportal.lirmm.fr}
+set :branch, ENV.include?('BRANCH') ? ENV['BRANCH'] : 'development'
 # Extended Server Syntax
 # ======================
 # This can be used to drop a more detailed server

From 48b2daf584d5b8292282a8ef0dabe22562e809f2 Mon Sep 17 00:00:00 2001
From: OntoPortal Bot <ontoportal.bot.lirmm@gmail.com>
Date: Mon, 16 Dec 2024 10:11:08 +0100
Subject: [PATCH 09/11] chagne test branch to development

---
 .github/workflows/deploy.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index a35bf88e..5626e6c4 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -20,7 +20,7 @@ on:
   push:
     branches:
       - stage
-      - test
+      - development
   # Allows running this workflow manually from the Actions tab
   workflow_dispatch:
     inputs:
@@ -29,7 +29,7 @@ on:
         type: choice
         options:
           - stage
-          - test
+          - development
           - master
         default: stage
         required: true

From 2b592551d5df8b871d26b18fe710c6eccd2cf727 Mon Sep 17 00:00:00 2001
From: OntoPortal Bot <ontoportal.bot.lirmm@gmail.com>
Date: Mon, 16 Dec 2024 11:47:41 +0100
Subject: [PATCH 10/11] update ontologies_linked_data in Gemfile.lock

---
 Gemfile.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index c0989308..4bcfba99 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -29,7 +29,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: c0f8697529ebfca2c3fe90d46d9482ac72f13362
+  revision: e3cf9888c2113152aaa250ee0cfaae37c534a53a
   branch: development
   specs:
     ontologies_linked_data (0.0.1)

From b762ebbcca080ebd733b96fcd86f0a5b50696c9c Mon Sep 17 00:00:00 2001
From: OntoPortal Bot <ontoportal.bot.lirmm@gmail.com>
Date: Mon, 16 Dec 2024 17:38:33 +0100
Subject: [PATCH 11/11] uncomment private_config_repo env variable

---
 config/deploy.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/deploy.rb b/config/deploy.rb
index b7d255a2..59c11707 100644
--- a/config/deploy.rb
+++ b/config/deploy.rb
@@ -42,7 +42,7 @@
 }
 
 # private git repo for configuraiton
-#PRIVATE_CONFIG_REPO = ENV.include?('PRIVATE_CONFIG_REPO') ? ENV['PRIVATE_CONFIG_REPO'] : 'https://your_github_pat_token@github.com/your_organization/ontoportal-configs.git'
+PRIVATE_CONFIG_REPO = ENV.include?('PRIVATE_CONFIG_REPO') ? ENV['PRIVATE_CONFIG_REPO'] : 'https://your_github_pat_token@github.com/your_organization/ontoportal-configs.git'
 desc "Check if agent forwarding is working"
 task :forwarding do
   on roles(:all) do |h|